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[191386_at]

Description C29A12.3 /REP_DB=WormBase Gene ID /WP=CE05328 /GEN=lig-1 /TR=SW:Q27474 /GB=CAA98242.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=DNA ligase I
Cluster 6grp_highest_10_10 > 78      6grp_high1_10_10 > 96      4grp_highest_8_8 > 18      4grp_high_8_8 > 62      6grp_highest_nonorm > 93      6grp_total > 87      4grp_total > 58      6grp_highest_sub > In      6grp_cgc > 58      6grp_high1_sub > In      6grp_cgc_sub > In      6grp_total_sub > Increase      6grp_rule_based > S6      4grp_rule_based > L3      

Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 110
1 2 3 4 range
A 280.5
(-1.3)
P 		284
(-1.1)
P 		338.1
(3)
P 		258.6
(-3)
P 		80
B 248.8
(-3)
P 		321
(3)
P 		308.3
(1.9)
P 		258.4
(-2.2)
P 		72
C 292.4
(1.3)
P 		289.3
(1.1)
P 		317.8
(3)
P 		227.9
(-3)
P 		90
avr 273.9
(-0.9) 		298.1
(1.1) 		321.4
(3) 		248.3
(-3) 		73

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 439
1 2 3 4 5 6 range
A 233.1
(-3)
P 		271.6
(-2.5)
P 		295.6
(-2.1)
P 		302.4
(-2)
P 		431.5
(-0.2)
P 		661.9
(3)
P 		429
B 223.3
(-3)
P 		246.7
(-2.6)
P 		242
(-2.7)
P 		331.5
(-1.3)
P 		395.3
(-0.3)
P 		600
(3)
P 		377
C 297.4
(-2.1)
P 		245
(-3)
P 		375.1
(-0.7)
P 		360.9
(-0.9)
P 		421.7
(0.2)
P 		579.7
(3)
P 		335
avr 251.3
(-3) 		254.4
(-2.9) 		304.2
(-2.1) 		331.6
(-1.7) 		416.2
(-0.3) 		613.9
(3) 		363
No Scale
G range Absolute graph Relative graph Expression Table Dauer Comp.
4 73
1 2 3 4 range
A 102.1
(3)
P 		61.6
(-0.8)
P 		88.4
(1.7)
P 		37.9
(-3)
P 		64
B 79.4
(3)
P 		79.3
(3)
P 		71.4
(1)
P 		55.1
(-3)
P 		24
C 96.8
(1.8)
P 		83.2
(0.7)
P 		110.8
(3)
P 		38.4
(-3)
P 		72
avr 92.8
(3) 		74.7
(0.8) 		90.2
(2.7) 		43.8
(-3) 		49

1 : 1 state (S1, L1)
2 : dauer (ST, LT)
6 181
1 2 3 4 5 6 range
A 43
(-3)
P 		96.6
(-0.3)
P 		64.4
(-1.9)
P 		76.7
(-1.3)
P 		130.2
(1.4)
P 		161.2
(3)
P 		118
B 77.7
(-2.3)
P 		82.1
(-2.2)
P 		58.8
(-3)
P 		87.8
(-1.9)
P 		160.6
(0.7)
P 		223.7
(3)
P 		165
C 110.2
(-1.1)
P 		74.8
(-2.9)
P 		95.5
(-1.9)
P 		72.6
(-3)
P 		136.5
(0.2)
P 		194.1
(3)
P 		122
avr 77
(-2.8) 		84.5
(-2.4) 		72.9
(-3) 		79
(-2.7) 		142.4
(0.5) 		193
(3) 		120
NetAffx Links Cluster Members
Consensus/Exemplar
GeneChip Array Information
Probe Set ID 191386_at
GeneChip Array C. elegans Genome Array
Organism Common Name Nematode
Probe Design Information
Transcript ID(Array Design) affy.Ce.13779
Sequence Type Exemplar sequence
Representative Public ID C29A12.3 NCBI
Target Description C29A12.3 /REP_DB=WormBase Gene ID /WP=CE05328 /GEN=lig-1 /TR=SW:Q27474 /GB=CAA98242.1 /SUBMIT=HINXTON /CHR=5 /FEA=Sanger Annotation /DEF=DNA ligase I
Cluster Evidence This cluster is supported by a Sanger Annotation.
Annotation Method Description
Annotation Description This probe set was annotated using the Matching Probes based pipeline to a RefSeq identifier using 1 transcript(s).
Annotation Grade This is a grade A annotation.
Annotation Transcript Cluster (# of Matching Probes) NM_171537(11)
Transcript Assignments
Representative
Transcript		 Description Matching Probes Related Probesets by Grade
NM_171537 NCBI Caenorhabditis elegans LIGase family member (lig-1) (lig-1) mRNA, complete cds. 11/11 None
SNAP00000008262 ENSEMBL cdna:SNAP chromosome:CEL140:V:10816699:10819209:1 9/11 None
GENEFINDER00000008271 ENSEMBL cdna:GeneFinder chromosome:CEL140:V:10816699:10819209:1 11/11 None
C29A12.3a ENSEMBL cdna:known chromosome:CEL140:V:10816699:10819301:1 gene:C29A12.3 11/11 None
Annotation Notes
There are no noteworthy cross hybridizing mRNAs found for this probe set.
Splice Variants
Entrez Total Refseq Isoforms Total Detected By This Probeset Refseq Probesets
179502 2 1 NM_171537 191386_at (11)
Genomic Alignment of Consensus/Exemplar Sequence
Assembly Wormbase March 2004
Alignment(s)
Position Identity Coverage Cytoband
chrV:10816476-10819209(+) 100.0 100.0
Public Domain and Genome References
Ensembl C29A12.3
Functional Annotations
Protein Similarities
Method ID Description E-Value
blast CAA98242 Hypothetical protein C29A12.3a [Caenorhabditis elegans] ref|NP_741625.2| LIGase family member (lig-1) [Caenorhabditis elegans] sp|Q27474|DNLI_CAEEL DNA ligase (Polydeoxyribonucleotide synthase [ATP]) 0.0
blast CAE64901 Hypothetical protein CBG09716 [Caenorhabditis briggsae] 0.0
blast XP_685041 PREDICTED: similar to ligase I [Danio rerio] 1.0E-172
Protein Domains
Database ID Description E-Value
Pfam IPR000977 EMBL-EBI ATP-dependent DNA ligase 8.1E-28
Pfam IPR000977 EMBL-EBI ATP-dependent DNA ligase 3.6E-100
Pfam IPR000977 EMBL-EBI ATP-dependent DNA ligase 4.3E-112
Sequence
Target Sequence 
>C. ELEGANS:191386_AT
gccgatattactatatctccgcgtcacaaagctgcaagtggattgacggatgatggaaaa
ggaatctctttgagatttcctcgtttcctgcgtattcgggacgataaaaattccgacgat
gcaacatcttcggagcaagttcttgaaatgtacaaaaaccaagaagcttttgccaaccag
aagatcgaaaaggcggatgcagttgatgaggatgacgaatttgaagaaaaagaagatgaa
gaggaggagttgaacatgaccaatgtatctgaaggaagttctaaagaaaatccagtgaaa
gaggagatcaagaaagagactcctaaatcagtatccccgaaaaaattcgaaaagaaaccg
cctgtaaaatcttcaccagttaacaaatcgcccgtgaaaagttcaccaataaagaaagaa
gcagagaaaaagaaaggaccagttgctagcatcttttcatcatcgacaaagaagaatgaa
aaagacgttaaagtggaatctccatctccgatcagaaagaagaagctgccttctgattct
gacgagtctga

BLASTn GenBank NR
Probe Info
Probe Sequence(5'-3') Probe X Probe Y Probe Interrogation
Position 		Strandedness
GCCGATATTACTATATCTCCGCGTC 553 283 1930 Antisense
ATCTCCGCGTCACAAAGCTGCAAGT 190 33 1944 Antisense
ATCTCTTTGAGATTTCCTCGTTTCC 278 33 1993 Antisense
CTCGTTTCCTGCGTATTCGGGACGA 620 231 2009 Antisense
GATGCAACATCTTCGGAGCAAGTTC 7 413 2047 Antisense
AAACCAAGAAGCTTTTGCCAACCAG 387 125 2085 Antisense
AGAGACTCCTAAATCAGTATCCCCG 678 67 2244 Antisense
GAAACCGCCTGTAAAATCTTCACCA 241 359 2283 Antisense
CTTCACCAGTTAACAAATCGCCCGT 290 219 2300 Antisense
TGCTAGCATCTTTTCATCATCGACA 74 581 2373 Antisense
TGCCTTCTGATTCTGACGAGTCTGA 134 585 2456 Antisense
Sequence Source Affymetrix Proprietary Database